Affiliations: 1: Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083-0688;
2: Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada

Received 01 January 2008Accepted 30 March 2008Published 07 October 2008

This review begins by briefly presenting the history of research on the chemical composition and other parameters of cells of E. coli and S. enterica at different exponential growth rates. Studies have allowed us to determine the in vivo strength of promoters and have allowed us to distinguish between factor-dependent transcriptional control of the promoter and changes in promoter activity due to changes in the concentration of free functional RNA polymerase associated with different growth conditions. The total, or bulk, amounts of RNA and protein are linked to the growth rate, because most bacterial RNA is ribosomal RNA (rRNA). Since ribosomes are required for protein synthesis, their number and their rate of function determine the rate of protein synthesis and cytoplasmic mass accumulation. Many mRNAs made in the presence of amino acids have strong ribosome binding sites whose presence reduces the expression of all other active genes. This implies that there can be profound differences in the spectrum of gene activities in cultures grown in different media that produce the same growth rate. Five classes of growth-related parameters that are generally useful in describing or establishing the macromolecular composition of bacterial cultures are described in detail in this review. A number of equations have been reported that describe the macromolecular composition of an average cell in an exponential culture as a function of the culture doubling time and five additional parameters: the C- and D-periods, protein per origin (PO), ribosome activity, and peptide chain elongation rate.

72.Koppes L, Nordstrom K.1986. Insertion of an R1 plasmid into the origin of replication of the E. coli chromosome: random timing of replication of the hybrid chromosome. Cell44:117–124.[PubMed][CrossRef]

This review begins by briefly presenting the history of research on the chemical composition and other parameters of cells of E. coli and S. enterica at different exponential growth rates. Studies have allowed us to determine the in vivo strength of promoters and have allowed us to distinguish between factor-dependent transcriptional control of the promoter and changes in promoter activity due to changes in the concentration of free functional RNA polymerase associated with different growth conditions. The total, or bulk, amounts of RNA and protein are linked to the growth rate, because most bacterial RNA is ribosomal RNA (rRNA). Since ribosomes are required for protein synthesis, their number and their rate of function determine the rate of protein synthesis and cytoplasmic mass accumulation. Many mRNAs made in the presence of amino acids have strong ribosome binding sites whose presence reduces the expression of all other active genes. This implies that there can be profound differences in the spectrum of gene activities in cultures grown in different media that produce the same growth rate. Five classes of growth-related parameters that are generally useful in describing or establishing the macromolecular composition of bacterial cultures are described in detail in this review. A number of equations have been reported that describe the macromolecular composition of an average cell in an exponential culture as a function of the culture doubling time and five additional parameters: the C- and D-periods, protein per origin (PO), ribosome activity, and peptide chain elongation rate.

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Figures

Modulation of Chemical Composition and Other Parameters of the Cell at Different Exponential Growth Rates

Relationships between growth rate, cell size, chromosome replication, transcription, and macromolecular composition. (Left) Average cell size (mass per cell, Table 2) for E. coli B/r growing with a doubling time, τ, ranging from 100 to 20 min (growth rate, μ, ranging from 0.6 to 3.0 doublings/h) is depicted by the shaded ovals. An idealized cell cycle with the major cell cycle events, ranging from cell age 0.0 (a newborn daughter cell) to 1.0 (a dividing mother cell), is presented for each growth rate. The position of an average cell of age 0.41 (defined so that 50% of the cells in the population are younger and 50% are older) is indicated by A. The cell ages at initiation (I) and termination (T) of chromosome replication are also indicated. The dashed portion of the age axis indicates a period during which there is no DNA replication (no replication forks on the chromosome). The light line portions represent periods where there are two forks per chromosome structure, and the heavy line portions indicate the age periods during which there are six forks per chromosome structure. After termination, there are two chromosome structures per cell, which are segregated to the daughter cells at the subsequent cell division (at age 1.0). (Center) Average structure of the replicating chromosome or chromosomes in the culture. For 24- and 20-min cell cycles (τ =24 or 20 min; bottom portion), the chromosome pattern indicates that replication has reinitiated and that each of these chromosome structures has multiple (six) replication forks. The amount of DNA in these structures in genome equivalents (G) is indicated (values from Table 2). The numbers of origins (O), termini (T), and forks (F) in this average genome are also indicated (from Table 2). (Right) The synthesis rates of rRNA (rR), tRNA (tR), r-protein mRNA (rpm), and other mRNA (om), expressed as a percent of total transcription, and the macromolecular composition are illustrated in bar graph form. The stable RNA fraction of the total transcription increases with increasing growth rate, the r-protein mRNA increases as a fraction of the total mRNA synthesis rate. Relative amounts of protein (P), DNA (D), RNA (R), and other components (O) as percent of the total cell mass are from the data in Table 2.

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Fig. 1.

Relationships between growth rate, cell size, chromosome replication, transcription, and macromolecular composition. (Left) Average cell size (mass per cell, Table 2) for E. coli B/r growing with a doubling time, τ, ranging from 100 to 20 min (growth rate, μ, ranging from 0.6 to 3.0 doublings/h) is depicted by the shaded ovals. An idealized cell cycle with the major cell cycle events, ranging from cell age 0.0 (a newborn daughter cell) to 1.0 (a dividing mother cell), is presented for each growth rate. The position of an average cell of age 0.41 (defined so that 50% of the cells in the population are younger and 50% are older) is indicated by A. The cell ages at initiation (I) and termination (T) of chromosome replication are also indicated. The dashed portion of the age axis indicates a period during which there is no DNA replication (no replication forks on the chromosome). The light line portions represent periods where there are two forks per chromosome structure, and the heavy line portions indicate the age periods during which there are six forks per chromosome structure. After termination, there are two chromosome structures per cell, which are segregated to the daughter cells at the subsequent cell division (at age 1.0). (Center) Average structure of the replicating chromosome or chromosomes in the culture. For 24- and 20-min cell cycles (τ =24 or 20 min; bottom portion), the chromosome pattern indicates that replication has reinitiated and that each of these chromosome structures has multiple (six) replication forks. The amount of DNA in these structures in genome equivalents (G) is indicated (values from Table 2). The numbers of origins (O), termini (T), and forks (F) in this average genome are also indicated (from Table 2). (Right) The synthesis rates of rRNA (rR), tRNA (tR), r-protein mRNA (rpm), and other mRNA (om), expressed as a percent of total transcription, and the macromolecular composition are illustrated in bar graph form. The stable RNA fraction of the total transcription increases with increasing growth rate, the r-protein mRNA increases as a fraction of the total mRNA synthesis rate. Relative amounts of protein (P), DNA (D), RNA (R), and other components (O) as percent of the total cell mass are from the data in Table 2.

Amounts and synthesis rates of molecular components in bacteria growing exponentially at rates between 0.6 and 2.5 doublings/h. The values of the RNA-to-protein (R/P; panel a) and DNA-to protein (G/P; panel b) ratios were calculated from lines 1, 2, and 3 in Table 2. The ribosome efficiency (i.e., the protein synthesis rate per average ribosome; panel c, left ordinate) was calculated from the number of ribosomes per cell (Table 3) and the rate of protein synthesis per cell. The latter was obtained fromthe amount of protein per cell (Table 2) using the first-order rate equation. The peptide chain elongation rates (panel c, right ordinate) are 1.25-fold higher than the ribosome efficiency values and account for the fact that only about 80%of the ribosomes are active at any instant. The fraction of the total RNA synthesis rate that is stable RNA ormRNA (rs or rm; panel d) is from line 5, Table 3. The rates of stable RNA and mRNA synthesis per amount of protein (rs/P or rm/P; panel e) were calculated from the data in Table 3, divided by the amount of protein per cell (Table 2). The ppGpp per protein value (ppGpp/P; panel f) is from Table 3. The cell age at which chromosome replication is initiated at oriC (ai in fractions of a generation; panel g) is calculated from C and D (Table 3) and equation 14 in Table 5. The protein (or mass) per cell at replication initiation (panel h) was calculated from the initiation age (ai; panel g) and the cell mass immediately after cell division (age zero; i.e., a = 0), using equation 17 in Table 5. The latter was obtained from the average protein or mass content of cells (lines 10 or 13, respectively; Table 2), using equation 16 of Table 5. The number of replication origins at the time of replication initiation (Oi; panel i) was obtained from the values of C and D (Table 3), using equation 15 of Table 5. The initiation mass (panel j), given as protein (or mass) per replication origin at the time of replication initiation, was obtained as the quotient of the values for Pi (or Mi) and Oi shown in panels h and i.

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Fig. 2.

Amounts and synthesis rates of molecular components in bacteria growing exponentially at rates between 0.6 and 2.5 doublings/h. The values of the RNA-to-protein (R/P; panel a) and DNA-to protein (G/P; panel b) ratios were calculated from lines 1, 2, and 3 in Table 2. The ribosome efficiency (i.e., the protein synthesis rate per average ribosome; panel c, left ordinate) was calculated from the number of ribosomes per cell (Table 3) and the rate of protein synthesis per cell. The latter was obtained fromthe amount of protein per cell (Table 2) using the first-order rate equation. The peptide chain elongation rates (panel c, right ordinate) are 1.25-fold higher than the ribosome efficiency values and account for the fact that only about 80%of the ribosomes are active at any instant. The fraction of the total RNA synthesis rate that is stable RNA ormRNA (rs or rm; panel d) is from line 5, Table 3. The rates of stable RNA and mRNA synthesis per amount of protein (rs/P or rm/P; panel e) were calculated from the data in Table 3, divided by the amount of protein per cell (Table 2). The ppGpp per protein value (ppGpp/P; panel f) is from Table 3. The cell age at which chromosome replication is initiated at oriC (ai in fractions of a generation; panel g) is calculated from C and D (Table 3) and equation 14 in Table 5. The protein (or mass) per cell at replication initiation (panel h) was calculated from the initiation age (ai; panel g) and the cell mass immediately after cell division (age zero; i.e., a = 0), using equation 17 in Table 5. The latter was obtained from the average protein or mass content of cells (lines 10 or 13, respectively; Table 2), using equation 16 of Table 5. The number of replication origins at the time of replication initiation (Oi; panel i) was obtained from the values of C and D (Table 3), using equation 15 of Table 5. The initiation mass (panel j), given as protein (or mass) per replication origin at the time of replication initiation, was obtained as the quotient of the values for Pi (or Mi) and Oi shown in panels h and i.

Effect of varying gene concentration on the total rate of RNA synthesis, the rate of transcription per gene, and the concentration of free RNA polymerase (from reference 60). The relationships are derived from an idealized cell, where all promoters are identical and the transcription times of all genes are equal. The volume of the cell is one unit and concentrations are given as numbers of molecules per cell. The cell contains 2,000 RNA polymerase molecules, and the number of promoters per cell [Pt] is varied between 0 and 400 (abscissa in all panels). Vmax is set at 30 initiations per minute per promoter, and Km is set at 200 RNA polymerase molecules per cell. All transcripts are 1,500 nucleotides long, and the RNA chain elongation rate is 50 nt/s. (a) The ordinate is the total steady-state rate of transcription, i = V · [Pt], measured as transcripts/min per cell. (b) The ordinate is the steady state rate, V, of transcription for one promoter measured as transcripts/min per promoter, calculated from equation 4 in reference 8. (c) The ordinate is the free RNA polymerase concentration, [Rf], calculated from equation 7 in reference 60. For panels b and c the ordinates are shown in log scale to illustrate how V and [Rf] approach zero as [Pt] increases and the total rate of transcription per cell, i, approaches its plateau value.

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Fig. 3.

Effect of varying gene concentration on the total rate of RNA synthesis, the rate of transcription per gene, and the concentration of free RNA polymerase (from reference 60). The relationships are derived from an idealized cell, where all promoters are identical and the transcription times of all genes are equal. The volume of the cell is one unit and concentrations are given as numbers of molecules per cell. The cell contains 2,000 RNA polymerase molecules, and the number of promoters per cell [Pt] is varied between 0 and 400 (abscissa in all panels). Vmax is set at 30 initiations per minute per promoter, and Km is set at 200 RNA polymerase molecules per cell. All transcripts are 1,500 nucleotides long, and the RNA chain elongation rate is 50 nt/s. (a) The ordinate is the total steady-state rate of transcription, i = V · [Pt], measured as transcripts/min per cell. (b) The ordinate is the steady state rate, V, of transcription for one promoter measured as transcripts/min per promoter, calculated from equation 4 in reference 8. (c) The ordinate is the free RNA polymerase concentration, [Rf], calculated from equation 7 in reference 60. For panels b and c the ordinates are shown in log scale to illustrate how V and [Rf] approach zero as [Pt] increases and the total rate of transcription per cell, i, approaches its plateau value.